A new method for detecting and interpreting biodiversity and ecological community thresholds

Abstract

Summary 1. Existing methods for identifying ecological community thresholds are designed for univariate indicators or multivariate dimension‐reduction of community structure. Most are insensitive to responses of individual taxa with low occurrence frequencies or highly variable abundances, properties of the vast majority of taxa in community data sets. We introduce Threshold Indicator Taxa ANalysis (TITAN) to detect changes in taxa distributions along an environmental gradient over space or time, and assess synchrony among taxa change points as evidence for community thresholds. 2. TITAN uses indicator species scores to integrate occurrence, abundance and directionality of taxa responses. It identifies the optimum value of a continuous variable, x, that partitions sample units while maximizing taxon‐specific scores. Indicator z scores standardize original scores relative to the mean and SD of permuted samples along x, thereby emphasizing the relative magnitude of change and increasing the contributions of taxa with low occurrence frequencies but high sensitivity to the gradient. TITAN distinguishes negative (z−) and positive (z+) taxa responses and tracks cumulative responses of declining [sum(z−)] and increasing [sum(z+)] taxa in the community. Bootstrapping is used to estimate indicator reliability and purity as well as uncertainty around the location of individual taxa and community change points. 3. Using two simulated data sets, TITAN correctly identified taxon and community thresholds in more than 99% of 500 unique versions of each simulation. In contrast, multivariate change‐point analysis did not distinguish directional taxa responses, resulting in much wider confidence intervals that in one instance failed to capture thresholds in 38% of the iterations. 4. Retrospective analysis of macroinvertebrate community response to a phosphorus gradient supported previous threshold estimates, although TITAN produced narrower confidence limits and revealed that several taxa declined at lower levels of phosphorus. Re‐analysis of macroinvertebrate responses to an urbanization gradient illustrated disparate change points for declining (0·81–3·3% urban land) and increasing (6·8–26·6%) taxa, whereas the published threshold estimate (20–30%) missed the declining‐taxa threshold because it could not distinguish their synchronous decline from the gradual increase in ubiquitous taxa. 5. Synthesis and applications. By deconstructing communities to assess synchrony of taxon‐specific change points, TITAN provides a sensitive and precise alternative to existing methods for assessing community thresholds. TITAN has tremendous potential to inform conservation of rare or threatened species, develop species sensitivity models, identify reference conditions and to support development of numerical regulatory criteria.

Water quality related macroinvertebrate community responses to environmental gradients in the Portoviejo River (Ecuador)

“…1000 permutations were used to determine species specific z-scores and related fsum(z)-scores, as this calculation is based on a small dataset, thus a higher number of permutations are recommended for more precise z-scores (Baker et al, 2015). Further information and details of the TITAN method can be found in Baker and King (2010), King and Baker (2014) and Baker et al (2015).…”

Indicators for taxonomic and functional aspects of biodiversity in the vineyard agroecosystem of Southern Switzerland

“…In the first step, we defined groups of sampling plots with more similar values for the above mentioned biodiversity indices (see Section 2.4). Then using the Threshold Indicator Taxa ANalysis (TITAN) approach (Baker and King, 2010), we detected and quantified community thresholds (sumz+ and sumzÀ) with regards to ''biodiversity gradients'' for each diversity index selected in our study. Sampling plots therefore fell into three groups: L (low), which indicates sampling plots with biodiversity values lower than the sumzÀ threshold, H (high) for those with biodiversity values higher than the sumz+ threshold and M (medium) those with biodiversity values between the sumzÀ and sumz+ thresholds.…”

“…For each of the six biodiversity indices, only plant species associated to H and combined M + H groups were considered as indicator species of 'high' and 'mid-to-high' taxonomic or functional biodiversity. The plant species cover percentage values were log-transformed in order to reduce the influence of highly variable taxa on the Indicator Value calculations as recommended by Baker and King (2010). Finally, to assess the degree of complementarity for each indicator species, we used the principal component analysis (PCA) based on the biodiversity indices that define a space of six dimensions and a PCA-plot to visualize the results.…”

“…The Threshold Indicator Taxa ANalysis was run with the package TITAN (Baker and King, 2010). The Indicator Value analysis (IndVal) complemented by the multi-levels pattern analysis was performed using a ''multipatt'' routine in the ''indicspecies '' package (De Cáceres and Legendre, 2009;De Cáceres et al, 2010).…”

Impact of nitrogen deposition at the species level

“…The critical load for this habitat is currently set at 10-15 kg N ha −1 y −1 , with three indicators of critical load exceedance: an increase in graminoids, a decrease in total species richness, and a decline of typical species (the indicator that we focus on here) (2). We apply Threshold Indicator Taxon Analysis (TITAN) to identify the points along the N deposition gradient at which individual plant species change in abundance (15) and compare these values with the critical load. TITAN identifies for each species the point along the N deposition gradient at which any systematic difference in cover is maximized (the change point), whether the difference in cover on either side of this change point is statistically significant, and if so, the abruptness of the difference.…”